Re: [AMBER] Antechamber preparartion

From: FyD <>
Date: Tue, 30 Oct 2012 09:35:31 +0100

Dear Alex,

You might be interested by the tools at
Charge values are based on ab initio computations.

q4md-forcefieldtools contains programs you can install on your
machine(s), a database of FF libraries, a server/cluster to perform
what you need and tutorials.

regards, Francois

> Hi, my name is Alex and I want to clarify several moments I had noted
> during Antechamber procedure.
> Q1. How to prepare a correct molecule of the inhibitor?
> Adding all hydrogenes - it is OK thanks to chemaxon and openbabel.
> Q2. But what about the inital conformation (is it important or I can use
> plane structure?) and atom type assignation (for example in PO3 group I
> have to use O.co2 atom type, as it is mentioned in tripos mol2 manual or
> )?
> Q3. Does it make reliable convertion from pdb ro mol2 or it is better to
> make some changes by hands in mol2 and then import it?
> Q4. What degree of accuracy this soft can provide? And, especially, what
> about biological molecule (derivatives) like ATP, modified amino acids?
> As I know developed for charmm27 had some problem with it.
> Q5. As I'm working with amber forcefield bith in gromacs4.5.5 and amber11
> I'm using AM1 bcc flag. So what about the string, is it correct?
> antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2

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Received on Tue Oct 30 2012 - 02:00:04 PDT
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